<div dir="ltr">Hi Manoj,<div><br></div><div>Thank you for reporting the issue and I'm sorry for the late reply.</div><div>I believe this issue is fixed now, so can you please try the latest nightly build (release candidate) from here:</div><div><a href="https://phenix-online.org/download/nightly_builds.cgi">https://phenix-online.org/download/nightly_builds.cgi</a><br></div><div><br></div><div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">So I was wondering if I can do this fix<br>in Phenix. Is this model idealization tool the best approach?</blockquote><div>You are welcome to try it out, it is designed to produce a good secondary structure with minimal deviation from the starting model and/or experimental density. Crucial part here would be to provide correct secondary structure annotations.</div><div> </div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"> or I have to go in and fix things manually.</blockquote><div>If everything else fails, this might be the last option. </div></div><div><br></div><div>Please let me know if you have any questions or issues. If you can share the data (off-list) I'm happy to look at it.</div><div><br></div><div>Best regards,</div><div>Oleg Sobolev.</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Tue, Jun 13, 2023 at 2:39 AM Manoj saxena <<a href="mailto:mks131@gmail.com">mks131@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div>Hi ,</div><div>I am trying to fix a pdb file that was obtained from Rosetta and has some distorted helices</div><div>so I trier to fix that with <br></div><div><br></div><div>> phenix.model_idealization model.pdb <span>use_ss_restraints</span><span> = True <br></span></div><div><span><br></span></div><div><span>I am attaching the log file , here is the end of the log file. Any suggestions on what's going on ?<br></span></div><div><span><br></span></div><div>" NOTE: a complete listing of the restraints can be obtained by requesting<br> output of .geo file.<br>Traceback (most recent call last):<br> File "/Applications/phenix-1.20.1-4487/build/../modules/cctbx_project/mmtbx/command_line/model_idealization.py", line 1118, in <module><br> run(sys.argv[1:])<br> File "/Applications/phenix-1.20.1-4487/build/../modules/cctbx_project/mmtbx/command_line/model_idealization.py", line 1106, in run<br> mi_object.run()<br> File "/Applications/phenix-1.20.1-4487/build/../modules/cctbx_project/mmtbx/command_line/model_idealization.py", line 548, in run<br> self._setup_model_h()<br> File "/Applications/phenix-1.20.1-4487/build/../modules/cctbx_project/mmtbx/command_line/model_idealization.py", line 478, in _setup_model_h<br> params_h.pdb_interpretation = self.model._pdb_interpretation_params.pdb_interpretation<br>AttributeError: 'NoneType' object has no attribute 'pdb_interpretation'"<br></div><div><span><br></span></div><div><span><br></span></div><div><span>My aim is to idealize the secondary structure. I first tried it in Isolde but the</span></div><div><span>EM density is not great and always leads to some distortion. So I was wondering if I can do this fix</span></div><div><span>in Phenix. Is this model idealization tool the best approach? or I have to go in and fix things manually.</span></div><div><span><br></span></div><div><span>Thanks</span></div><div><span>Manoj<br></span></div></div>
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